The landscape of allelic expression and DNA methylation at the bovine SGCE/PEG10 locus

Abstract Genomic imprinting is an epigenetic regulation in mammals in which a small subset of genes is monoallelically expressed dependent on their parental origin. A large imprinted domain, SGCE/PEG10 locus, is located on human chromosome 7q21s and mouse proximal chromosome 6. However, genomic imprinting of bovine SGCE/PEG10 cluster has not been systematically studied. In this study, we investigated allele expression of 14 genes of the SGCE/PEG10 locus in bovine somatic tissues and term placenta using a single nucleotide polymorphism (SNP)‐based sequencing method. In addition to SGCE and PEG10 , two conserved paternally expressed genes in human and mice, five other genes ( TFPI2 , GNG11 , ASB4 , PON1 , and PON3 ) were paternally expressed. Three genes, BET1 , COL1A2 , and CASD1 , exhibited tissue‐specific monoallelic expression. CALCR showed monoallelic expression in tissues but biallelic expression in the placenta. Three genes, GNGT1 , PPP1R9A , and PON2 , showed biallelic expression in cattle. Five differentially methylated regions (DMRs) were found to be associated with the allelic expression of TFPI2 , COL1A2 , SGCE/PEG10 , PON3 , and ASB4 genes, respectively. The SGCE/PEG10 DMR is a maternally hypermethylated germline DMR, but TFPI2 , COL1A2 , PON3 , and ASB4 DMRs are secondary DMRs. In summary, we identified five novel bovine imprinted genes ( GNG11 , BET1 , COL1A2 , CASD1 , and PON1 ) and four secondary DMRs at the SGCE/PEG10 locus.